r28117 - in /trunk/test_suite/system_tests: scripts/structure/pca_observers.py structure.py -- November 25, 2015 - 18:38

Author: bugman
Date: Wed Nov 25 18:38:34 2015
New Revision: 28117

URL: http://svn.gna.org/viewcvs/relax?rev=28117&view=rev
Log:
Created the Structure.test_pca_observers system test.

This is for testing the new observer structures concept of the structure.pca 
user function.

Added:
    trunk/test_suite/system_tests/scripts/structure/pca_observers.py
Modified:
    trunk/test_suite/system_tests/structure.py

Added: trunk/test_suite/system_tests/scripts/structure/pca_observers.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/structure/pca_observers.py?rev=28117&view=auto
==============================================================================
--- trunk/test_suite/system_tests/scripts/structure/pca_observers.py    
(added)
+++ trunk/test_suite/system_tests/scripts/structure/pca_observers.py    Wed 
Nov 25 18:38:34 2015
@@ -0,0 +1,31 @@
+# Python module imports.
+from os import sep
+
+# relax imports.
+from data_store import Relax_data_store; ds = Relax_data_store()
+from status import Status; status = Status()
+
+
+# Missing temp directory (allow this script to run outside of the system 
test framework).
+if not hasattr(ds, 'tmpdir'):
+    ds.tmpdir = 'temp_script'
+
+# Create a data pipe.
+pipe.create('pca test', 'N-state')
+
+# Load the structures.
+path = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'pca'
+structure.read_pdb('distribution.pdb', dir=path, read_mol=1, 
set_mol_name='CaM A')
+structure.read_pdb('distribution.pdb', dir=path, read_mol=4, 
set_mol_name='CaM A', merge=True)
+
+# Create a reference structure.
+pipe.create('ref', 'N-state')
+structure.read_pdb('distribution.pdb', dir=path, read_mol=1, read_model=1, 
set_mol_name='CaM A')
+structure.translate([10.0, 10.0, 10.0])
+pipe.switch('pca test')
+
+# PCA analysis.
+structure.pca(pipes=['pca test', 'ref'], obs_pipes=['ref'], dir=ds.tmpdir)
+
+# Save the program state.
+state.save(force=True, dir=ds.tmpdir)

Modified: trunk/test_suite/system_tests/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=28117&r1=28116&r2=28117&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py  (original)
+++ trunk/test_suite/system_tests/structure.py  Wed Nov 25 18:38:34 2015
@@ -4161,6 +4161,37 @@
                 self.assertAlmostEqual(cdp.structure.pca_proj[mode, struct], 
proj[struct, mode], 4)
 
 
+    def test_pca_observers(self):
+        """Test the principle component analysis of the structure.pca user 
function while using observer molecules."""
+
+        # Execute the script.
+        self.script_exec(status.install_path + 
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'structure'+sep+'pca_observers.py')
+
+        # The Gromacs values (converted from nm to Angstrom).
+        values = array([0.417808, 0.0164377, 0.000675256, 1.17952e-05], 
float64) * 100
+        proj = array([
+            [-0.38735,  0.21143, -0.02325, -0.00119],
+            [ 0.96087,  0.07893,  0.02651,  0.00209],
+            [-0.84236, -0.05173,  0.03651, -0.00140],
+            [-0.23302, -0.11191, -0.02209,  0.00530],
+            [ 0.50186, -0.12672, -0.01767, -0.00481]
+        ], float64) * 10
+
+        # Invert the 3rd and 4th Gromacs eigenvectors to match.
+        proj[:, 2] = -proj[:, 2]
+        proj[:, 3] = -proj[:, 3]
+
+        # Checks.
+        self.assert_(hasattr(cdp.structure, 'pca_values'))
+        self.assert_(hasattr(cdp.structure, 'pca_vectors'))
+        self.assert_(hasattr(cdp.structure, 'pca_proj'))
+        self.assertEqual(len(cdp.structure.pca_values), 4)
+        for mode in range(4):
+            self.assertAlmostEqual(cdp.structure.pca_values[mode], 
values[mode], 5)
+            for struct in range(5):
+                self.assertAlmostEqual(cdp.structure.pca_proj[mode, struct], 
proj[struct, mode], 4)
+
+
     def test_pdb_combined_secondary_structure(self):
         """Test the handling of secondary structure metadata when combining 
multiple PDB structures."""